in progress

[jalview.git] / forester / java / src / org / forester / archaeopteryx / MainFrameApplication.java

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index b1688a3..d6fe0f6 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -65,6 +65,7 @@ import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
 import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
 import org.forester.archaeopteryx.tools.GoAnnotation;
+import org.forester.archaeopteryx.tools.InferenceManager;
 import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
 import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
 import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
@@ -241,6 +242,7 @@ public final class MainFrameApplication extends MainFrame {
                                   final Configuration config,
                                   final String title,
                                   final File current_dir ) {
+        super();
         _configuration = config;
         if ( _configuration == null ) {
             throw new IllegalArgumentException( "configuration is null" );
@@ -677,13 +679,12 @@ public final class MainFrameApplication extends MainFrame {
     }
 
     void buildPhylogeneticInferenceMenu() {
+        final InferenceManager inference_manager = InferenceManager.getInstance();
         _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
-        _inference_menu
-                .add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment...(EXPERIMENTAL - DO NOT USE!!) " ) );
+        _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
         customizeJMenuItem( _inference_from_msa_item );
         _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
-        _inference_menu
-                .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences...(EXPERIMENTAL - DO NOT USE!!) " ) );
+        _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
         customizeJMenuItem( _inference_from_seqs_item );
         _inference_from_seqs_item.setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
         _jmenubar.add( _inference_menu );
@@ -1113,7 +1114,7 @@ public final class MainFrameApplication extends MainFrame {
                 phy.hashIDs();
                 phy.recalculateNumberOfExternalDescendants( true );
                 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
-                getCurrentTreePanel().updateSetOfCollapsedExternalNodes( phy );
+                getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
                 getCurrentTreePanel().calculateLongestExtNodeInfo();
                 getCurrentTreePanel().setNodeInPreorderToNull();
                 getCurrentTreePanel().recalculateMaxDistanceToRoot();